Package fr.ens.biologie.genomique.eoulsan.util.r

Class AbstractRExecutor

java.lang.Object

fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

All Implemented Interfaces:

RExecutor

Direct Known Subclasses:

ProcessRExecutor, RserveRExecutor

public abstract class AbstractRExecutor
extends Object
implements RExecutor

This class define an abstract RExecutor.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractRExecutor(File outputDirectory, File temporaryDirectory)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
protected abstract void	executeRScript(File rScriptFile, boolean sweave, String sweaveOuput, File workflowOutputDir, String... scriptArguments)	Execute a R script.
void	executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)	Execute a R script.
protected File	getOutputDirectory()	Get the output directory of the analysis.
void	getOutputFiles()	Get the output files of the analysis
protected File	getTemporaryDirectory()	Get the temporary directory.
void	openConnection()	Open the connection.
protected abstract void	putFile(DataFile inputFile, String outputFilename)	Put a file for the analysis.
void	putInputFile(DataFile inputFile)	Put a file for the analysis.
void	putInputFile(DataFile inputFile, String outputFilename)	Put a file.
protected abstract void	removeFile(String filename)	Remove a file of the analysis.
void	removeInputFiles()	Remove input files.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor

getName, writerFile

Constructor Detail

AbstractRExecutor

protected AbstractRExecutor(File outputDirectory,
                            File temporaryDirectory)
                     throws IOException

Constructor.

Parameters:

outputDirectory - output directory

Throws:

IOException - if the output directory does not exists

Method Detail

putFile

protected abstract void putFile(DataFile inputFile,
                                String outputFilename)
                         throws IOException

Put a file for the analysis.

Parameters:

inputFile - the input file

outputFilename - the output filename

Throws:

IOException - if an error occurs while putting the file

removeFile

protected abstract void removeFile(String filename)
                            throws IOException

Remove a file of the analysis.

Parameters:

filename - the filename of the file to remove

Throws:

IOException - if the removing of the file fails

executeRScript

protected abstract void executeRScript(File rScriptFile,
                                       boolean sweave,
                                       String sweaveOuput,
                                       File workflowOutputDir,
                                       String... scriptArguments)
                                throws IOException

Execute a R script.

Parameters:

rScriptFile - The R script file

sweave - execute the R using Sweave

sweaveOuput - sweave output file

scriptArguments - script arguments

Throws:

IOException - if an error occurs while executing the script

getOutputDirectory

protected File getOutputDirectory()

Get the output directory of the analysis.

Returns:

the output directory of the analysis

getTemporaryDirectory

protected File getTemporaryDirectory()

Get the temporary directory.

Returns:

the temporary directory

openConnection

public void openConnection()
                    throws IOException

Description copied from interface: RExecutor

Open the connection.

Specified by:

openConnection in interface RExecutor

Throws:

IOException - if an error occurs while opening the connection

closeConnection

public void closeConnection()
                     throws IOException

Description copied from interface: RExecutor

Close the connection.

Specified by:

closeConnection in interface RExecutor

Throws:

IOException - if an error occurs while closing the connection

getOutputFiles

public void getOutputFiles()
                    throws IOException

Description copied from interface: RExecutor

Get the output files of the analysis

Specified by:

getOutputFiles in interface RExecutor

Throws:

IOException - if an error occurs while getting the output files

putInputFile

public void putInputFile(DataFile inputFile)
                  throws IOException

Description copied from interface: RExecutor

Put a file for the analysis.

Specified by:

putInputFile in interface RExecutor

Parameters:

inputFile - the input file

Throws:

IOException - if an error occurs while putting the file

putInputFile

public void putInputFile(DataFile inputFile,
                         String outputFilename)
                  throws IOException

Description copied from interface: RExecutor

Put a file.

Specified by:

putInputFile in interface RExecutor

Parameters:

inputFile - the file to put

outputFilename - the output filename

Throws:

IOException - if an exception occurs while putting a file

removeInputFiles

public void removeInputFiles()
                      throws IOException

Description copied from interface: RExecutor

Remove input files.

Specified by:

removeInputFiles in interface RExecutor

Throws:

IOException - if an error occurs while removing the files

executeRScript

public void executeRScript(String rScript,
                           boolean sweave,
                           String sweaveOutput,
                           boolean saveRscript,
                           String description,
                           DataFile workflowOutputDir,
                           String... scriptArguments)
                    throws IOException

Description copied from interface: RExecutor

Execute a R script.

Specified by:

executeRScript in interface RExecutor

Parameters:

rScript - the source of the script to execute

sweave - true if the script is a Sweave script

sweaveOutput - Sweave output file

saveRscript - true to keep the R script

description - description of the R script

workflowOutputDir - workflow output directory

scriptArguments - script arguments

Throws:

IOException - if an error occurs while executing the script